PROJECT SUMMARY/ABSTRACT Over the last decade, oncology has served as a paragon for the application of clinical genomics towards the diagnosis and treatment of disease. The availability of high-throughput technologies for clinical assessment, coupled with emerging knowledge of the genomic aberrations that promote the growth and progression of tumors, has revolutionized cancer medicine. In 2014, we initiated a prospective clinical sequencing initiative to examine 341 (now 468) cancer associated genes in tumor and matched normal specimens from patients with advanced cancer, a cohort which now exceeds 25,000. We have used these data to identify and report somatic mutations to facilitate enrollment to genomically matched clinical trials and pathogenic germline alleles to reveal familial cancer susceptibility. Yet, we lack a fundamental understanding regarding the extent to which germline alterations promote and interact with somatic mutations to affect cancer progression and response to therapy. There remains a transformative opportunity to integrate germline and somatic analysis to further inform prognosis and treatment decisions. Moreover, somatic mutational patterns and signatures can be harnessed to discover novel germline alleles of biological and clinical significance. Here, we propose to build upon our unique prospective clinical sequencing initiative to gain a comprehensive picture of how germline and somatic alterations interact to influence cancer initiation, progression and therapeutic response. Building upon extensive Preliminary Data, we will pursue this goal through 3 specific aims: (1) establish the prevalence of germline risk alleles and associated patterns of somatic mutations across cancers; (2) establish integrated germline-somatic clinical biomarkers of tumor progression and response to DNA repair agents; (3) discover novel candidate pathogenic alleles of biological and clinical significance. Within the timeframe of this grant, we will sequence tumor-normal pairs from >70,000 patients under active treatment, providing an unprecedented opportunity to identify and rigorously evaluate germline-somatic interactions and their relevance to clinical practice. We will leverage the rich genomic and clinical data set collected through our existing clinical sequencing initiative to identify pathogenic germline variants, tumor-specific zygosity changes, and co-occurring patterns of somatic mutations in all solid tumor types. By integrating clinical annotations, family history and outcome data with the alterations identified in each patient, we will identify novel functional alleles and clinically significant biomarkers of disease- specific outcomes and therapeutic response. The lessons we learn here will facilitate new clinical guidelines and diagnostic approaches for cancer patients and establish best practices for discovering and clinically validating prognostic and predictive biomarkers at the intersection of germline and somatic genetics.